Molecular and paleontological approaches have produced extremely different estimates for divergence times among orders of placental mammals and within rodents with molecular studies suggesting a much older date than fossils. We evaluated the conflict between the fossil record and molecular data and find a significant correlation between dates estimated by fossils and relative branch lengths, suggesting that molecular data agree with the fossil record regarding divergence times in rodents. Our approach includes a correction for tree hierarchy involving simulating the random appearance of fossils. We also present a ghost lineage approach that attempts to incorporate the potential for the discovery of older fossils into a Bayesian analysis of divergence dates. Applying this approach to a set of Eocene rodent fossils, we estimated the earliest divergence in rodents appears to have occurred at approximately the K/T boundary, but interordinal splits were estimated to have taken place late in the Cretaceous. We propose that some molecular clock studies may overestimate divergence times due to periods of accelerated molecular evolution across multiple lineages or due to saturation of data that is not adequately corrected by the evolutionary model. We have sequenced the complete mitochondrial genomes of three rodent species, Anomalurus beecrofti, Castor canadensis, and Dipodomys ordii, and attempt to resolve phylogenetic relationships within rodents using the mitochondrial genome, a nuclear dataset of comparable size, and a combined analysis containing 26 kbp of sequence data. The combined analysis recovered a Sciuromorpha – Hystricomorpha clade with strong support. Our data suggest that increased character sampling improves resolution at these early nodes while better taxon sampling of mitochondrial genomes has led to better supported clades that converge on conclusions obtained from nuclear datasets. Several molecular studies have concluded that the zokors, genus Myospalax, evolved from within the rodent subfamily Cricetinae. We tested this conclusion using mitochondrial data and determined that Myospalax is sister to a clade containing the subfamilies Spalacinae and Rhizomyinae, and all three of these lineages appear to be basal to the superfamily Muroidea. Based on the position of these three lineages, we suggested that they be placed in a distinct family, the Spalacidae. The murine genera Mus and Rattus are thought to have diverged about 12 million years ago (Ma) based on a series of fossils from the Siwaliks of Pakistan, but assumptions of murid relationships that led to this conclusion have been shown to be false by molecular data. Equally parsimonious hypotheses can be proposed which place the 12 million year old Progonomys fossil at the base of the family Muridae, basal to the subfamily Murinae, or at the Mus - Rattus divergence. We here test the dates of evolutionary divergences in murids. Our results indicate that the family Muridae probably diverged earlier than the Siwalik fossils, but Mus and Rattus diverged at the same time or prior to the 12 Ma fossil date. We also cannot reject the hypothesis that the 12 Ma date represents the oldest split in the Murinae instead of the more derived Mus – Rattus date. We also recovered phylogenetic results suggesting that Taterillus is related to the tribe Gerbillini and not to other genera that are treated as Taterillini and that Gerbillurus evolved from within Gerbilliscus.

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A ( diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

Teasing apart the evolutionary forces responsible for biological phenomena is difficult in the absence of a detailed evolutionary history, especially if this history is lacking a temporal component. RNA viruses, due to their rapid rate of molecular and phenotypic evolution, provide a unique biological system in which to study the temporal aspects of evolutionary processes. These types of studies are possible because of relaxed molecular clock dating techniques, which allow the rate of evolution to vary across a phylogenetic tree. The primary focus of the research presented here concerns the age of the simian immunodeficiency virus (SIV), the primate precursor to HIV. SIV has long been thought to be an ancient infection in non-human African primates, and it has been hypothesized that codivergence with its primate hosts has shaped the SIV phylogeny and resulted in a virus capable of apathogenic infection. The codivergence theory was tested by comparing the phylogeny of a group of monkeys thought to be exemplary of SIV-host codivergence to the phylogeny of their SIVs (Appendix A). These phylogenies were incongruent, suggesting that SIV may have infected these monkeys after their common ancestor speciated. The codivergence theory was investigated further by estimating the time of most recent common ancestor for the SIV lineages that directly gave rise to HIV, found in sooty mangabeys and chimpanzees (Appendix B). The temporal estimates suggest that these SIV lineages are only of hundreds of years old, much younger than expected under the codivergence hypothesis. Next, the same dating techniques were employed to elucidate the evolutionary history of an emerging RNA virus of shrimp, Taura syndrome virus (Appendix C). This analysis provided phylogenetic confirmation that Taura syndrome virus emerged out of the Americas and spread rapidly around the world. Finally, because all of these studies utilized relaxed molecular clocks, a simulation study was performed to test the hypothesis that relaxed molecular clocks provide higher quality phylogenetic inference compared with traditional time-free phylogenetic inference (Appendix D). This simulation found no difference in the overall quality of phylogenetic inference between these methods.

To test competing hypotheses about the relative roles of vicariance and dispersal in the freshwater fishes in Galaxiidae, a phylogenetic framework and a time scale for species divergence were estimated using mitochondrial and nuclear DNA sequences. Relaxed clock dating revealed that the Galaxiidae originated in Gondwana in the late Cretaceous and thus vicariance cannot be ruled out for the two basal lineages, Galaxiella and Brachygalaxias. These two lineages are ancient relicts that rafted to their present distributions or were fragmented by the separation of Australia from South America via Antarctica. The opening of the Drake passage between South America and Antarctica initiated the proto-Antarctic Circumpolar Current (pACC) and counter-clockwise circulation in the South Atlantic, on which marine stage ancestors could have dispersed to South Africa and New Zealand via Australia during the late Eocene. Thus dispersal explains the disjunct distribution of the clade comprised of G. platei, G. zebratus and Neochanna spp. in South America, South Africa, and Australasia. The narrowing of the Drake passage and collapse of the pACC from about 24-14 Mya likely prevented further contact between South America and South Africa. Tectonic events around the globe produced an anomalous warming event, which along with the uplift of New Zealand provided empty niches and promoted the radiation of Galaxias. Most of the speciation in the other clades occurred during this time. When the Antarctic Circumpolar Current was reactivated at the end of the Mid-Miocene Climatic Optimum (MMCO) about 15–14 Mya, it provided a marine conveyor belt for the dispersal of the ancestor of Galaxias maculatus from Australia to South America, and later to Australia and New Zealand. The integration of divergence times estimated on the phylogeny with ancestral area reconstruction supports an origin in Gondwana and subsequent oceanic dispersal as the explanation for the distribution of the Galaxiidae across the southern continents.

To test competing hypotheses about the relative roles of vicariance and dispersal in the freshwater fishes in Galaxiidae, a phylogenetic framework and a time scale for species divergence were estimated using mitochondrial and nuclear DNA sequences. Relaxed clock dating revealed that the Galaxiidae originated in Gondwana in the late Cretaceous and thus vicariance cannot be ruled out for the two basal lineages, Galaxiella and Brachygalaxias. These two lineages are ancient relicts that rafted to their present distributions or were fragmented by the separation of Australia from South America via Antarctica. The opening of the Drake passage between South America and Antarctica initiated the proto-Antarctic Circumpolar Current (pACC) and counter-clockwise circulation in the South Atlantic, on which marine stage ancestors could have dispersed to South Africa and New Zealand via Australia during the late Eocene. Thus dispersal explains the disjunct distribution of the clade comprised of G. platei, G. zebratus and Neochanna spp. in South America, South Africa, and Australasia. The narrowing of the Drake passage and collapse of the pACC from about 24-14 Mya likely prevented further contact between South America and South Africa. Tectonic events around the globe produced an anomalous warming event, which along with the uplift of New Zealand provided empty niches and promoted the radiation of Galaxias. Most of the speciation in the other clades occurred during this time. When the Antarctic Circumpolar Current was reactivated at the end of the Mid-Miocene Climatic Optimum (MMCO) about 15–14 Mya, it provided a marine conveyor belt for the dispersal of the ancestor of Galaxias maculatus from Australia to South America, and later to Australia and New Zealand. The integration of divergence times estimated on the phylogeny with ancestral area reconstruction supports an origin in Gondwana and subsequent oceanic dispersal as the explanation for the distribution of the Galaxiidae across the southern continents.

DNA methylation is an epigenetic modification in which a methyl group is covalently added to the DNA. In vertebrate genomes methylation occurs almost exclusively at cytosines immediately followed by a guanine (CpG dinucleotides). Two important aspects of DNA methylation have inspired several recent scientific investigations including those in this dissertation. First, methylated cytosines are hotspots of point mutation due to a methylation-dependent mutation mechanism, which has caused a deficiency of CpGs in vertebrate genomes. Second, DNA methylation in promoters is linked with transcriptional silencing of the associated genes. This dissertation presents the results of four studies in which I investigated the impacts of DNA methylation on the neutral and functional evolution of vertebrate genomes. The results of the first two studies demonstrate that DNA methylation has profound impacts on both inter- and intra-genomic neutral substitution rate variation. The third and fourth studies demonstrate that DNA methylation has played critical roles in shaping the evolution of vertebrate promoters and gene regulation.

The suprachiasmatic nucleus (SCN) of the anterior hypothalamus has long been considered a master circadian pacemaker that drives rhythms in physiology and behavior in mammals. The recent discovery of self-sustained and cell-autonomous circadian oscillators in peripheral tissues has challenged this position. This dissertation tested the general hypothesis that the SCN has properties that distinguish it from other oscillators, thereby positioning it atop a circadian hierarchy. The general approach was to compare the consequences of altering the molecular circadian clock on tissue-autonomous rhythmicity in mice. In the first experiments, the role of the SCN as a master clock was tested by manipulating the expression of a circadian gene in the brain. Specifically, the expression of the short period tau mutation of casein kinase-1-epsilon (CK1ε) was controlled in an anatomically- and a temporally-specific manner via a tetracycline transactivator regulatory system. This inducible expression of CK1εtau affected the period of activity rhythms when expressed in the SCN, but did not affect the tissue-autonomous rhythmic properties in the peripheral tissues. Second, real-time bioluminescence imaging of tissues from PER2::LUCIFERASE mice revealed that period and phase of different circadian oscillators were tissue specific. Various circadian gene mutations (Cry1-/-, Cry2-/-, Cry1-/-;Cry2-/-, Clock∆19/∆19) produced little difference in rhythmic properties between the SCN and peripheral oscillators, although Cry1-/- SCN had more robust and persistent rhythms compared with the periphery. Third, the loss of Bmal1, which produces behavioral arrhythmicity, eliminated rhythms in the peripheral tissues, but not in the SCN. Bmal1-/- SCN rhythms were highly variable in period and amplitude, fitting a stochastic, but not a deterministic model of rhythm generation. Unlike mutations in other circadian genes, rhythmicity was completely abolished in single SCN neurons in Bmal1-/- mice, indicating that rhythms in Bmal1-/- SCN tissue are a property of the tissue organization rather than an averaging of single-cell autonomous rhythms. The SCN, therefore, has a unique anatomical organization that contributes to long-term stability and temporal organization of the circadian hierarchy.

Among the number of examples of broad radiations of insects on plants, the fig fig wasp system is one of the most remarkable. Although this interaction has frequently been used as a model for studies of mutualism and coevolution, other groups of insects associated with fig trees have received less attention. The weevils (Coleoptera: Curculionidae) associated with figs are one notable example. Being the largest family of animals, weevils achieved great evolutionary success due to their early association with their host plants. Despite few reports in literature, there is strong evidence of the specialization of weevils on figs. The main objective of this thesis was to understand how diversification of Curculionidae took place in fig trees. Previous studies have never addressed the systematics and biogeography of fig weevils under a phylogenetic framework. Therefore, we analyzed the tempo of diversification of Curculionidae lineages that use fig trees as host in order to reconstruct their historical biogeography. To gather information on fig weevils, we collected 325 fruit sets from more than 12% of the total Ficus species, from the Neotropical, Afrotropical and Oriental regions. We also examined seven entomological collections (AMNH, BMNH, INBIO, MNHN, MZUSP, NMNH, SAMC) searching for weevil specimens collected on figs. At least 80 weevil species from five genera (Cetatopus, Omophorus, Carponinus, Curculio, and Indocurculio) were found to be associated with figs. The radiation of curculionids on figs occurred at least three times independently. The tempo of diversification of the crown fig weevils is congruent with the diversification of figs during the Upper-Cretaceous/Lower-Eocene period. We hypothesize that the variation of the sea level and warmer climate in the past had great influence on the evolution of the species. Our results encourage future research on the biology and ecology of these species and will help us to understand the role weevils may have played in the evolution of the fig- fig wasp mutualism. / Um dos mais notáveis exemplos de radiação adaptativa de insetos em classes de plantas é o sistema figueiras - vespas de figo. Embora essa interação tenha sido frequentemente usada como modelo nos estudos de mutualismo e coevolução, outros grupos de insetos relacionados às figueiras têm sido negligenciados. Besouros curculionídeos (Coleoptera: Curculionidae) associados a figueiras representam um desses grupos pouco estudados. Apesar dos relatos escassos na literatura, existem fortes evidências do alto grau de especialização destes besouros às suas plantas hospedeiras. O objetivo geral desta tese foi entender como se deu a diversificação dos curculionídeos sobre as figueiras. Trabalhos anteriores nunca utilizaram uma abordagem filogenética para estudar a sistemática e biogeografia dos curculionídeos de figo e, por isso, este estudo analisa o tempo de diversificação das linhagenes destes besouros para reconstruir sua biogeografia histórica. De modo a obter informações das espécies estudadas, foram coletadas 325 amostras de frutos de cerca de 12% do total de espécies de figueiras das regiões Neotropical, Afrotropical e Oriental. Sete coleções entomológicas (AMNH, BMNH, INBIO, MNHN, MZUSP, NMNH, SAMC) foram vistadas em busca de espécimes de curculionídeos coletados em figo. Pelo menos 80 espécies de cinco gêneros (Cetatopus, Omophorus, Carponinus, Curculio e Indocurculio) foram encontradas. A radiação dos curculionídeos de figo ocorreu independentemente pelo menos três vezes ao longo da história dos Curculionidae. O período de diversificação das linhagenes de curculionídeos de figo é fortemente congruente com o período de diversificação das linhagenes de figueiras durante o fim do Cretáceo/Paleoceno. Acredita-se que fatores como a forte variação no nível dos oceanos e o clima mais quente no passado tiveram grande influência na evolução das espécies. Espera-se que os resultados deste trabalho encorajem estudos futuros sobre a biologia e ecologia dos curculionídeos associados às figueiras e auxilie no entendimento do papel que os curculionídeos possam ter desempenhado na evolução do sistema Ficus - vespas de figo.

In dieser Arbeit wurde die Systematik und Evolution der Viviparidae (Mollusca, Gastropoda, Caenogastropoda) mit einem Fokus auf den asiatischen Gattungen untersucht. Es wurde die erste umfassende gattungsübergreifende Phylogenie der Gruppe mit Vertretern von mehr als 70% der bekannten Viviparidengattungen durch die Analyse eines molekularen Datensatzes aus mitochondrialen wie auch nukleären Sequenzen rekonstruiert. Die Einteilung in die aufgrund von anatomischen Merkmalen beschriebenen Unterfamilien konnte durch die genetischen Untersuchungen bestätigt werden. Neben der molekularen Systematik stand auch die Aufklärung der historischen Biogeographie der Viviparidae im Fokus. Mithilfe von Fossilbelegen und der Anwendung einer molekularen Uhr wurde die Diversifikation dieser Familie in Raum und Zeit untersucht. Abschätzungen über das Alter der Abspaltungen der wichtigsten Abstammungslinien innerhalb der Viviparidae mittels der molekularen Uhr lassen sowohl Vikarianz- als auch Dispersal-Ereignisse am Zustandekommen heutiger Verbreitungsmuster erkennen. Die bisherige systematische Gliederung der Viviparidae ist ausschließlich durch einen conchologischen Ansatz geprägt. Bei der Untersuchung zur Evolution der Schale, unter Berücksichtigung der molekularen Ergebnisse, zeigt sich jedoch, dass eine klare Ordnung innerhalb der Vivipariden, bezogen auf die Entstehung von Farbbändern oder Skulpturierungen auf der Schalenoberfläche, nicht zu erkennen ist. Scheinbar komplexe Schalenmerkmale entstanden mehrfach unabhängig in unterschiedlichen Linien. Es konnte hier aber auch gezeigt werden, dass die Untersuchung von anatomischen Merkmalen im Vergleich zur Schale wesentlich besser geeignet ist, natürliche Verwandtschaftsbeziehungen zu erkennen. Die in dieser Arbeit gewonnenen Ergebnisse schaffen die Grundlage für eine in Zukunft nötige Revision der Familie Viviparidae auf Gattungsebene. / This thesis focusses on the systematics and evolution of Viviparidae (Mollusca, Gastropoda, Caenogastropoda), a large and putatively ancient group of ovoviviparous freshwater gastropods with an almost worldwide distribution. With more than 200 described species with highly disparate shells, Asia and Australia have the highest viviparid diversity. Three genetic markers where used to calculate the first molecular phylogeny comprising more than 70% of all extant viviparid genera which provides new insights into the systematics and biogeography of this diverse group of freshwater snails. The traditional division into three subfamilies (Lioplacinae Gill, 1863, Viviparinae Gray, 1847 and Bellamyinae Rohrbach, 1937), based on anatomical data, is supported by the molecular phylogeny. The taxonomy of the Asian taxa is still largely based on shell morphology and rather inconsistent, though, making it difficult to gain deeper insights into their evolution and biogeography at present. The molecular phylogeny presented here indicates that the current shell morphology-based viviparid taxonomy does not reflect the phylogenetic relationships of species and clades. In addition to the focus on molecular systematics, a major part of this thesis is devoted to elucidating the historical biogeography of viviparids. A molecular clock analysis based on a calibration scheme using fossils of varying age and taxonomic affinity was used to yield divergence time estimates for the major viviparid lineages. Ancestral areas were inferred by parsimony and likelihood analyses. Viviparid distribution patterns have been shaped by both dispersal and vicariance events. The study of anatomical features turned out to be considerably better approach for establishing phylogenetic relationships of viviparids, manifested in good support of genera established by molecular data. The results obtained in this work provide the basis for a much needed revision of the Viviparidae at the generic level.

The suprachiasmatic nucleus (SCN) of the anterior hypothalamus has long been considered a master circadian pacemaker that drives rhythms in physiology and behavior in mammals. The recent discovery of self-sustained and cell-autonomous circadian oscillators in peripheral tissues has challenged this position. This dissertation tested the general hypothesis that the SCN has properties that distinguish it from other oscillators, thereby positioning it atop a circadian hierarchy. The general approach was to compare the consequences of altering the molecular circadian clock on tissue-autonomous rhythmicity in mice. In the first experiments, the role of the SCN as a master clock was tested by manipulating the expression of a circadian gene in the brain. Specifically, the expression of the short period tau mutation of casein kinase-1-epsilon (CK1ε) was controlled in an anatomically- and a temporally-specific manner via a tetracycline transactivator regulatory system. This inducible expression of CK1εtau affected the period of activity rhythms when expressed in the SCN, but did not affect the tissue-autonomous rhythmic properties in the peripheral tissues. Second, real-time bioluminescence imaging of tissues from PER2::LUCIFERASE mice revealed that period and phase of different circadian oscillators were tissue specific. Various circadian gene mutations (Cry1-/-, Cry2-/-, Cry1-/-;Cry2-/-, Clock∆19/∆19) produced little difference in rhythmic properties between the SCN and peripheral oscillators, although Cry1-/- SCN had more robust and persistent rhythms compared with the periphery. Third, the loss of Bmal1, which produces behavioral arrhythmicity, eliminated rhythms in the peripheral tissues, but not in the SCN. Bmal1-/- SCN rhythms were highly variable in period and amplitude, fitting a stochastic, but not a deterministic model of rhythm generation. Unlike mutations in other circadian genes, rhythmicity was completely abolished in single SCN neurons in Bmal1-/- mice, indicating that rhythms in Bmal1-/- SCN tissue are a property of the tissue organization rather than an averaging of single-cell autonomous rhythms. The SCN, therefore, has a unique anatomical organization that contributes to long-term stability and temporal organization of the circadian hierarchy.